Tuesday, 29 March 2011

DNA close up

I wanted to look a little bit more at the details of the DNA structure. In part motivated by James Watson's book (described here). Some time ago I showed pictures of the helix, but now I want to show some molecular details.[1]

This is the backbone of DNA in its B-form. The phosphate is in front. The 2-deoxyribose is the vertical 5-ring. Its anomeric center is bonded to the nitrogen of the base and the oxygen closing the furanose ring. The 3' oxygen bonds to the next phosphate group. The 5' oxygen leading to the other side is bonded to the carbon outside of the ring.

In principle a pentose has five active groups. In DNA all are saturated and no OH groups remain. Why?
1' bonded to the nitrogen
2' that's the "deoxy" in "deoxy-ribonucleic acid"
3' bonded to phosphate
4' forming the ring
5' bonded to phosphate

What happens if we put an OH group at the 2' position?

The new OH groups is shown with its full van-der-Waals radius. There is clearly not enough room for the extra oxygen atom, considering for example that the other oxygen atoms should be just as big. It is in fact not possible to push the atoms out of the way in any simple manner. Therefore RNA does not form a B-helix.

The structures were created with the nucleic functionality of Tinker. The pictures were drawn with pymol.


[1] One thing I really learned in science is quoting myself ...

Sunday, 6 March 2011

Traveling to Texas

It is my third time at a research institution in the USA, this time at Texas Tech. The first good impression was that when I filled out my "Electronic System for Travel Authorization" form, they told me I did not even have to fill it out because I was already authorized - and that even though last time I went to the US there was not even such an electronic system. That's good administration. When I got there this somewhat changed after waiting in line for an hour while my connecting flight was leaving. Even worse was that when it was finally my turn I was a little bit detained because I did not know if I was "visiting" or "researching". Why would you do all the J1 bureaucracy if you are just visiting a group to make some personal contacts? Anyway the second guy told me that it was no problem and I could enter.

What I really like about US universities is that they are trying to make them nice and productive places. The campus looks nice and when you go to your office it looks like it is all prepared with the idea in mind to make an open environment for good research. Back in Vienna we are in a building that was planned to be torn down 20 years ago. For example we do not have enough places to put up our posters, which I always think is sad. The only thing they did to improve our work is putting in new fire doors and some ugly new pipes for fire extinguishers. I am not saying it is not necessary to have protection against fires but I don't like the idea that everyting is built upon formal fire protection rules rather and no-one even thinks about what kind of measures would be important to provide a productive research environment.

The US mentality toward research is something that really motivates me to come here. But then some other things kind of strike me. Here it is mostly the huge abundance of SUVs and pick-up trucks. It makes me wonder what it is that people are trying to compensate ... But it's ok I guess, if for some people a stretch limo is the only way they can find a mate, aside from dangerous penis enlargement surgery, then I guess it is socially just that stretch limos exist. Or is it more the mentality of the type: "With all those crazy people out there driving SUVs, you'd better get the biggest car that you can!" Anyway, on most of the side streets car drivers are much more polite than I am used to in Vienna, so it's ok.

The step that follows after traveling is of course reimbursement, as described nicely at PhD comics (1,2). You give a free loan, collect tons of paperwork and then you carry it to the financial department on your knees. We even have to show our credit card statements - my opinion is: if they want a credit card statement, they should also give me a credit card and everything is solved. But what can I do. Interestingly the hosting US institutions were always much more generous, insisting on paying some extra food money, without really so much bureaucracy. But I think guests at our department at home also do not have to do all the paperwork. So it seems like departments always treat their guests better than their own people.